grapholscape/dist/grapholscape.esm.min.js

ontology visualization

/**
 * MIT License
 *
 * Copyright (c) 2018-2024 OBDA Systems
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 */

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y=v[0]*s[0]+e,m=v[0]*s[1]+t;return v.length>1?v[0]==v[1]?[y,m]:[y,m,v[1]*s[0]+e,v[1]*s[1]+t]:[y,m]},rn=function(e,t,n){return t<=e&&e<=n||n<=e&&e<=t?e:e<=t&&t<=n||n<=t&&t<=e?t:n},on=function(e,t,n,i,r,o,a,s,l){var c=e-r,u=n-e,d=a-r,h=t-o,p=i-t,g=s-o,f=d*h-g*c,v=u*h-p*c,y=g*u-d*p;if(0!==y){var m=f/y,b=v/y,w=-.001;return w<=m&&m<=1.001&&w<=b&&b<=1.001||l?[e+m*u,t+m*p]:[]}return 0===f||0===v?rn(e,n,a)===a?[a,s]:rn(e,n,r)===r?[r,o]:rn(r,a,n)===n?[n,i]:[]:[]},an=function(e,t,n,i,r,o,a,s){var l,c,u,d,h,p,g=[],f=new Array(n.length),v=!0;if(null==o&&(v=!1),v){for(var y=0;y<f.length/2;y++)f[2*y]=n[2*y]*o+i,f[2*y+1]=n[2*y+1]*a+r;if(s>0){var m=en(f,-s);c=Kt(m)}else c=f}else c=n;for(var b=0;b<c.length/2;b++)u=c[2*b],d=c[2*b+1],b<c.length/2-1?(h=c[2*(b+1)],p=c[2*(b+1)+1]):(h=c[0],p=c[1]),0!==(l=on(e,t,i,r,u,d,h,p)).length&&g.push(l[0],l[1]);return g},sn=function(e,t,n){var i=[e[0]-t[0],e[1]-t[1]],r=Math.sqrt(i[0]*i[0]+i[1]*i[1]),o=(r-n)/r;return 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t=gn(e),n=t.dampingFactor,i=t.precision,r=t.iterations,o=t.weight,a=this._private.cy,s=this.byGroup(),l=s.nodes,c=s.edges,u=l.length,d=u*u,h=c.length,p=new Array(d),g=new Array(u),f=(1-n)/u,v=0;v<u;v++){for(var y=0;y<u;y++){p[v*u+y]=0}g[v]=0}for(var m=0;m<h;m++){var b=c[m],w=b.data("source"),x=b.data("target");if(w!==x){var _=l.indexOfId(w),E=l.indexOfId(x),T=o(b);p[E*u+_]+=T,g[_]+=T}}for(var C=1/u+f,S=0;S<u;S++)if(0===g[S])for(var I=0;I<u;I++){p[I*u+S]=C}else for(var O=0;O<u;O++){var N=O*u+S;p[N]=p[N]/g[S]+f}for(var P,A=new Array(u),k=new Array(u),R=0;R<u;R++)A[R]=1;for(var L=0;L<r;L++){for(var D=0;D<u;D++)k[D]=0;for(var M=0;M<u;M++)for(var $=0;$<u;$++){var B=M*u+$;k[M]+=p[B]*A[$]}Rt(k),P=A,A=k,k=P;for(var z=0,V=0;V<u;V++){var F=P[V]-A[V];z+=F*F}if(z<i)break}return{rank:function(e){return e=a.collection(e)[0],A[l.indexOf(e)]}}}},vn=Ke({root:null,weight:function(e){return 1},directed:!1,alpha:0}),yn={degreeCentralityNormalized:function(e){e=vn(e);var t=this.cy(),n=this.nodes(),i=n.length;if(e.directed){for(var r={},o={},a=0,s=0,l=0;l<i;l++){var c=n[l],u=c.id();e.root=c;var d=this.degreeCentrality(e);a<d.indegree&&(a=d.indegree),s<d.outdegree&&(s=d.outdegree),r[u]=d.indegree,o[u]=d.outdegree}return{indegree:function(e){return 0==a?0:(m(e)&&(e=t.filter(e)),r[e.id()]/a)},outdegree:function(e){return 0===s?0:(m(e)&&(e=t.filter(e)),o[e.id()]/s)}}}for(var h={},p=0,g=0;g<i;g++){var f=n[g];e.root=f;var v=this.degreeCentrality(e);p<v.degree&&(p=v.degree),h[f.id()]=v.degree}return{degree:function(e){return 0===p?0:(m(e)&&(e=t.filter(e)),h[e.id()]/p)}}},degreeCentrality:function(e){e=vn(e);var t=this.cy(),n=this,i=e,r=i.root,o=i.weight,a=i.directed,s=i.alpha;if(r=t.collection(r)[0],a){for(var l=r.connectedEdges(),c=l.filter((function(e){return e.target().same(r)&&n.has(e)})),u=l.filter((function(e){return e.source().same(r)&&n.has(e)})),d=c.length,h=u.length,p=0,g=0,f=0;f<c.length;f++)p+=o(c[f]);for(var v=0;v<u.length;v++)g+=o(u[v]);return{indegree:Math.pow(d,1-s)*Math.pow(p,s),outdegree:Math.pow(h,1-s)*Math.pow(g,s)}}for(var y=r.connectedEdges().intersection(n),m=y.length,b=0,w=0;w<y.length;w++)b+=o(y[w]);return{degree:Math.pow(m,1-s)*Math.pow(b,s)}}};yn.dc=yn.degreeCentrality,yn.dcn=yn.degreeCentralityNormalised=yn.degreeCentralityNormalized;var mn=Ke({harmonic:!0,weight:function(){return 1},directed:!1,root:null}),bn={closenessCentralityNormalized:function(e){for(var t=mn(e),n=t.harmonic,i=t.weight,r=t.directed,o=this.cy(),a={},s=0,l=this.nodes(),c=this.floydWarshall({weight:i,directed:r}),u=0;u<l.length;u++){for(var d=0,h=l[u],p=0;p<l.length;p++)if(u!==p){var g=c.distance(h,l[p]);d+=n?1/g:g}n||(d=1/d),s<d&&(s=d),a[h.id()]=d}return{closeness:function(e){return 0==s?0:(e=m(e)?o.filter(e)[0].id():e.id(),a[e]/s)}}},closenessCentrality:function(e){var t=mn(e),n=t.root,i=t.weight,r=t.directed,o=t.harmonic;n=this.filter(n)[0];for(var a=this.dijkstra({root:n,weight:i,directed:r}),s=0,l=this.nodes(),c=0;c<l.length;c++){var u=l[c];if(!u.same(n)){var d=a.distanceTo(u);s+=o?1/d:d}}return o?s:1/s}};bn.cc=bn.closenessCentrality,bn.ccn=bn.closenessCentralityNormalised=bn.closenessCentralityNormalized;var wn=Ke({weight:null,directed:!1}),xn={betweennessCentrality:function(e){for(var t=wn(e),n=t.directed,i=t.weight,r=null!=i,o=this.cy(),a=this.nodes(),s={},l={},c=0,u=function(e,t){l[e]=t,t>c&&(c=t)},d=function(e){return l[e]},h=0;h<a.length;h++){var p=a[h],g=p.id();s[g]=n?p.outgoers().nodes():p.openNeighborhood().nodes(),u(g,0)}for(var f=function(e){for(var t=a[e].id(),n=[],l={},c={},h={},p=new dt((function(e,t){return h[e]-h[t]})),g=0;g<a.length;g++){var f=a[g].id();l[f]=[],c[f]=0,h[f]=1/0}for(c[t]=1,h[t]=0,p.push(t);!p.empty();){var v=p.pop();if(n.push(v),r)for(var y=0;y<s[v].length;y++){var m=s[v][y],b=o.getElementById(v),w=void 0;w=b.edgesTo(m).length>0?b.edgesTo(m)[0]:m.edgesTo(b)[0];var x=i(w);m=m.id(),h[m]>h[v]+x&&(h[m]=h[v]+x,p.nodes.indexOf(m)<0?p.push(m):p.updateItem(m),c[m]=0,l[m]=[]),h[m]==h[v]+x&&(c[m]=c[m]+c[v],l[m].push(v))}else for(var _=0;_<s[v].length;_++){var E=s[v][_].id();h[E]==1/0&&(p.push(E),h[E]=h[v]+1),h[E]==h[v]+1&&(c[E]=c[E]+c[v],l[E].push(v))}}for(var T={},C=0;C<a.length;C++)T[a[C].id()]=0;for(;n.length>0;){for(var S=n.pop(),I=0;I<l[S].length;I++){var O=l[S][I];T[O]=T[O]+c[O]/c[S]*(1+T[S])}S!=a[e].id()&&u(S,d(S)+T[S])}},v=0;v<a.length;v++)f(v);var y={betweenness:function(e){var t=o.collection(e).id();return d(t)},betweennessNormalized:function(e){if(0==c)return 0;var t=o.collection(e).id();return d(t)/c}};return y.betweennessNormalised=y.betweennessNormalized,y}};xn.bc=xn.betweennessCentrality;var _n=Ke({expandFactor:2,inflateFactor:2,multFactor:1,maxIterations:20,attributes:[function(e){return 1}]}),En=function(e,t){for(var n=0,i=0;i<t.length;i++)n+=t[i](e);return n},Tn=function(e,t){for(var n,i=0;i<t;i++){n=0;for(var r=0;r<t;r++)n+=e[r*t+i];for(var o=0;o<t;o++)e[o*t+i]=e[o*t+i]/n}},Cn=function(e,t,n){for(var i=new Array(n*n),r=0;r<n;r++){for(var o=0;o<n;o++)i[r*n+o]=0;for(var a=0;a<n;a++)for(var s=0;s<n;s++)i[r*n+s]+=e[r*n+a]*t[a*n+s]}return i},Sn=function(e,t,n){for(var i=e.slice(0),r=1;r<n;r++)e=Cn(e,i,t);return e},In=function(e,t,n){for(var i=new Array(t*t),r=0;r<t*t;r++)i[r]=Math.pow(e[r],n);return Tn(i,t),i},On=function(e,t,n,i){for(var r=0;r<n;r++){if(Math.round(e[r]*Math.pow(10,i))/Math.pow(10,i)!==Math.round(t[r]*Math.pow(10,i))/Math.pow(10,i))return!1}return!0},Nn=function(e,t){for(var n=0;n<e.length;n++)if(!t[n]||e[n].id()!==t[n].id())return!1;return!0},Pn=function(e){for(var t=this.nodes(),n=this.edges(),i=this.cy(),r=function(e){return _n(e)}(e),o={},a=0;a<t.length;a++)o[t[a].id()]=a;for(var s,l=t.length,c=l*l,u=new Array(c),d=0;d<c;d++)u[d]=0;for(var h=0;h<n.length;h++){var p=n[h],g=o[p.source().id()],f=o[p.target().id()],v=En(p,r.attributes);u[g*l+f]+=v,u[f*l+g]+=v}!function(e,t,n){for(var i=0;i<t;i++)e[i*t+i]=n}(u,l,r.multFactor),Tn(u,l);for(var y=!0,m=0;y&&m<r.maxIterations;)y=!1,s=Sn(u,l,r.expandFactor),u=In(s,l,r.inflateFactor),On(u,s,c,4)||(y=!0),m++;var b=function(e,t,n,i){for(var r=[],o=0;o<t;o++){for(var a=[],s=0;s<t;s++)Math.round(1e3*e[o*t+s])/1e3>0&&a.push(n[s]);0!==a.length&&r.push(i.collection(a))}return r}(u,l,t,i);return b=function(e){for(var t=0;t<e.length;t++)for(var n=0;n<e.length;n++)t!=n&&Nn(e[t],e[n])&&e.splice(n,1);return e}(b),b},An={markovClustering:Pn,mcl:Pn},kn=function(e){return e},Rn=function(e,t){return Math.abs(t-e)},Ln=function(e,t,n){return e+Rn(t,n)},Dn=function(e,t,n){return e+Math.pow(n-t,2)},Mn=function(e){return Math.sqrt(e)},$n=function(e,t,n){return Math.max(e,Rn(t,n))},Bn=function(e,t,n,i,r){for(var o=arguments.length>5&&void 0!==arguments[5]?arguments[5]:kn,a=i,s=0;s<e;s++)a=r(a,t(s),n(s));return o(a)},zn={euclidean:function(e,t,n){return e>=2?Bn(e,t,n,0,Dn,Mn):Bn(e,t,n,0,Ln)},squaredEuclidean:function(e,t,n){return Bn(e,t,n,0,Dn)},manhattan:function(e,t,n){return Bn(e,t,n,0,Ln)},max:function(e,t,n){return Bn(e,t,n,-1/0,$n)}};function Vn(e,t,n,i,r,o){var a;return a=b(e)?e:zn[e]||zn.euclidean,0===t&&b(e)?a(r,o):a(t,n,i,r,o)}zn["squared-euclidean"]=zn.squaredEuclidean,zn.squaredeuclidean=zn.squaredEuclidean;var Fn=Ke({k:2,m:2,sensitivityThreshold:1e-4,distance:"euclidean",maxIterations:10,attributes:[],testMode:!1,testCentroids:null}),qn=function(e){return Fn(e)},jn=function(e,t,n,i,r){var o="kMedoids"!==r?function(e){return n[e]}:function(e){return i[e](n)},a=n,s=t;return Vn(e,i.length,o,(function(e){return i[e](t)}),a,s)},Hn=function(e,t,n){for(var i=n.length,r=new Array(i),o=new Array(i),a=new Array(t),s=null,l=0;l<i;l++)r[l]=e.min(n[l]).value,o[l]=e.max(n[l]).value;for(var c=0;c<t;c++){s=[];for(var u=0;u<i;u++)s[u]=Math.random()*(o[u]-r[u])+r[u];a[c]=s}return a},Un=function(e,t,n,i,r){for(var o=1/0,a=0,s=0;s<t.length;s++){var l=jn(n,e,t[s],i,r);l<o&&(o=l,a=s)}return a},Gn=function(e,t,n){for(var i=[],r=null,o=0;o<t.length;o++)n[(r=t[o]).id()]===e&&i.push(r);return i},Yn=function(e,t,n){return Math.abs(t-e)<=n},Qn=function(e,t,n){for(var i=0;i<e.length;i++)for(var r=0;r<e[i].length;r++){if(Math.abs(e[i][r]-t[i][r])>n)return!1}return!0},Zn=function(e,t,n){for(var i=0;i<n;i++)if(e===t[i])return!0;return!1},Wn=function(e,t){var n=new Array(t);if(e.length<50)for(var i=0;i<t;i++){for(var r=e[Math.floor(Math.random()*e.length)];Zn(r,n,i);)r=e[Math.floor(Math.random()*e.length)];n[i]=r}else for(var o=0;o<t;o++)n[o]=e[Math.floor(Math.random()*e.length)];return n},Xn=function(e,t,n){for(var i=0,r=0;r<t.length;r++)i+=jn("manhattan",t[r],e,n,"kMedoids");return i},Jn=function(e,t,n,i,r){for(var o,a,s=0;s<t.length;s++)for(var l=0;l<e.length;l++)i[s][l]=Math.pow(n[s][l],r.m);for(var c=0;c<e.length;c++)for(var u=0;u<r.attributes.length;u++){o=0,a=0;for(var d=0;d<t.length;d++)o+=i[d][c]*r.attributes[u](t[d]),a+=i[d][c];e[c][u]=o/a}},Kn=function(e,t,n,i,r){for(var o=0;o<e.length;o++)t[o]=e[o].slice();for(var a,s,l,c=2/(r.m-1),u=0;u<n.length;u++)for(var d=0;d<i.length;d++){a=0;for(var h=0;h<n.length;h++)s=jn(r.distance,i[d],n[u],r.attributes,"cmeans"),l=jn(r.distance,i[d],n[h],r.attributes,"cmeans"),a+=Math.pow(s/l,c);e[d][u]=1/a}},ei=function(e){var t,n,i,r,o,a=this.cy(),s=this.nodes(),l=qn(e);r=new Array(s.length);for(var c=0;c<s.length;c++)r[c]=new Array(l.k);i=new Array(s.length);for(var u=0;u<s.length;u++)i[u]=new Array(l.k);for(var d=0;d<s.length;d++){for(var h=0,p=0;p<l.k;p++)i[d][p]=Math.random(),h+=i[d][p];for(var g=0;g<l.k;g++)i[d][g]=i[d][g]/h}n=new Array(l.k);for(var f=0;f<l.k;f++)n[f]=new Array(l.attributes.length);o=new Array(s.length);for(var v=0;v<s.length;v++)o[v]=new Array(l.k);for(var y=!0,m=0;y&&m<l.maxIterations;)y=!1,Jn(n,s,i,o,l),Kn(i,r,n,s,l),Qn(i,r,l.sensitivityThreshold)||(y=!0),m++;return t=function(e,t,n,i){for(var r,o,a=new Array(n.k),s=0;s<a.length;s++)a[s]=[];for(var l=0;l<t.length;l++){r=-1/0,o=-1;for(var c=0;c<t[0].length;c++)t[l][c]>r&&(r=t[l][c],o=c);a[o].push(e[l])}for(var u=0;u<a.length;u++)a[u]=i.collection(a[u]);return a}(s,i,l,a),{clusters:t,degreeOfMembership:i}},ti={kMeans:function(e){var t,i=this.cy(),r=this.nodes(),o=null,a=qn(e),s=new Array(a.k),l={};a.testMode?"number"==typeof a.testCentroids?(a.testCentroids,t=Hn(r,a.k,a.attributes)):t="object"===n(a.testCentroids)?a.testCentroids:Hn(r,a.k,a.attributes):t=Hn(r,a.k,a.attributes);for(var c=!0,u=0;c&&u<a.maxIterations;){for(var d=0;d<r.length;d++)l[(o=r[d]).id()]=Un(o,t,a.distance,a.attributes,"kMeans");c=!1;for(var h=0;h<a.k;h++){var p=Gn(h,r,l);if(0!==p.length){for(var g=a.attributes.length,f=t[h],v=new Array(g),y=new Array(g),m=0;m<g;m++){y[m]=0;for(var b=0;b<p.length;b++)o=p[b],y[m]+=a.attributes[m](o);v[m]=y[m]/p.length,Yn(v[m],f[m],a.sensitivityThreshold)||(c=!0)}t[h]=v,s[h]=i.collection(p)}}u++}return s},kMedoids:function(e){var t,i,r=this.cy(),o=this.nodes(),a=null,s=qn(e),l=new Array(s.k),c={},u=new Array(s.k);s.testMode?"number"==typeof s.testCentroids||(t="object"===n(s.testCentroids)?s.testCentroids:Wn(o,s.k)):t=Wn(o,s.k);for(var d=!0,h=0;d&&h<s.maxIterations;){for(var p=0;p<o.length;p++)c[(a=o[p]).id()]=Un(a,t,s.distance,s.attributes,"kMedoids");d=!1;for(var g=0;g<t.length;g++){var f=Gn(g,o,c);if(0!==f.length){u[g]=Xn(t[g],f,s.attributes);for(var v=0;v<f.length;v++)(i=Xn(f[v],f,s.attributes))<u[g]&&(u[g]=i,t[g]=f[v],d=!0);l[g]=r.collection(f)}}h++}return l},fuzzyCMeans:ei,fcm:ei},ni=Ke({distance:"euclidean",linkage:"min",mode:"threshold",threshold:1/0,addDendrogram:!1,dendrogramDepth:0,attributes:[]}),ii={single:"min",complete:"max"},ri=function(e,t,n,i,r){